Desmond — Minimization Panel

The Minimization panel allows you to set up and submit jobs that relax a system into a local energy minimum, using a Brownian motion simulation.

To open this panel: click the Tasks button and browse to Desmond → Minimization.

  • Using
  • Features
  • Additional Resources

Using the Minimization Panel

The Minimization panel is designed to make setting up jobs as easy as possible. The main panel provides the most common simulation controls, while the Advanced Options dialog box provides access to a larger range of parameters. The default values represent a good balance between accuracy and performance and work for most jobs without change, but can be changed as needed.

To run a minimization job:

  1. Specify the model system, either by loading it from the Maestro Workspace or importing it from a file.

  2. Choose Minimization from the Simulation task option menu.

  3. Adjust the simulation parameters as necessary.

    For parameters that are not available in the main panel, open the Advanced Options dialog box.

  4. Choose Job Settings from the Settings button menu,

    set the job parameters in the Job Settings dialog box, and click Run to run the job.

To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button and choose Write. For information on command usage and options, see multisim Command Help.

Minimization Panel Features

Model system section

In this section, you select the model system that you will use for the simulation. A valid model system must contain both the coordinates of the particles and the force field parameters. A file of a valid model system normally has the .cms extension. You can use the System Builder Panel to prepare the model system for any structure that you have. If you want to build an amorphous structure from scratch, you can use the Disordered System Builder Panel to create a model system.

The option menu offers two choices for the source of the model system:

  • Load from Workspace—Load the model system from the Workspace. When you choose this option, the Load button is displayed to the right of the menu. Click this button to load the model system.

  • Import from file—Import the model system from a file. When you choose this option, a text box and Browse button are displayed to the right of the menu. You can enter the name of the file in the text box, or click Browse and navigate to the file.

    You can choose to import a model system file (.cms) or a checkpoint file (.cpt).

    If you import a model system file, it must contain a model system that has already been prepared. When the file is imported, a message about the system is displayed below the option menu.

    If you import a checkpoint file, most of the panel controls are unavailable. The purpose of the checkpoint file is to restart an interrupted simulation, so the parameters of the simulation cannot be altered. You can change the total simulation time, and then start the job.

Minimization section

In this section, you make settings for the Brownian motion simulation.

Simulation time text box

Enter the maximum simulation time for the Brownian motion simulation, in ps.

Advanced Options button

Opens the Advanced Options dialog box, in which you can control many more of the detailed settings for the minimization than are available in the Minimization panel.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

Status bar

The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.

Use the Reset button to reset the panel to its default settings and clear any data from the panel. You can also reset the panel from the Job toolbar.

The status bar also contains the Help button , which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.

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